When an agent creates a ticket it is assumed the ticket came in by phone. There is some logic to that.
When you receive an email, and forward it to your support site it will be recorded as Source = Email.
I don't think there is a lot you can do about this (don't shoot the messenger, I don't work for Freshdesk). There is a request to be able to change the status code (no longer possible in Mint). I suggest you support that request.